def generate_canonical_rotamer_residues_phipsi(residue_name3, target_phi_psi):
raise NotImlementedError
canonical_residue = generate_canonical_residue(residue_name3)
test_sequence = "AAX[%s]AA" % residue_name3
target_phi, target_psi = target_phi_psi
sf = get_score_function()
tryrot = TryRotamers(resnum=3,
scorefxn=sf,
explosion=0,
jump_num=0,
clash_check=True,
solo_res=False,
include_current=False)
test_pose = Pose()
make_pose_from_sequence(test_pose, test_sequence, "fa_standard")
for i in range(1, test_pose.size() + 1):
test_pose.set_psi(i, target_psi)
test_pose.set_phi(i, target_phi)
test_pose.set_omega(i, 180)
tryrot.setup_rotamer_set(test_pose)
rotamer_set = tryrot.rotamer_set()
# print('rotamer_set.num_rotamers()',
# residue_name3, target_phi_psi, rotamer_set.num_rotamers())
rotamers = [
rotamer_set.rotamer(i).clone()
for i in range(1,
rotamer_set.num_rotamers() + 1)
]
for r in rotamers:
r.orient_onto_residue(canonical_residue)
r.seqpos(1)
return rotamers
def pose_from_sequence(seq, res_type="fa_standard", auto_termini=True):
"""
Returns a pose generated from a single-letter sequence of amino acid
residues in <seq> using the <res_type> ResidueType and creates N- and C-
termini if <auto_termini> is set to True.
Unlike make_pose_from_sequence(), this method generates a default PDBInfo
and sets all torsion angles to 180 degrees.
Example:
pose = pose_from_sequence("THANKSEVAN")
See also:
Pose
make_pose_from_sequence()
pose_from_file()
pose_from_rcsb()
"""
pose = Pose()
make_pose_from_sequence(pose, seq, res_type, auto_termini)
#print 'Setting phi, psi, omega...'
for i in range(0, pose.total_residue()):
res = pose.residue(i + 1)
if not res.is_protein() or res.is_peptoid() or res.is_carbohydrate():
continue
pose.set_phi(i + 1, 180)
pose.set_psi(i + 1, 180)
pose.set_omega(i + 1, 180)
#print 'Attaching PDBInfo...'
# Empty PDBInfo (rosetta.core.pose.PDBInfo()) is not correct here;
# we have to reserve space for atoms....
pose.pdb_info(rosetta.core.pose.PDBInfo(pose))
pose.pdb_info().name(seq[:8])
# print pose
return pose